I'd like to deploy a
learnr tutorial to teach students how to explore and interpret
DESeq2 output (a package for analyzing genomic / RNA-seq data). But if I just add
library(DESeq2) to a
learnr tutorial, shinyapps.io runs out of memory.
To be clear, I'm not trying to run the
DESeq2 analysis on shinyapps.io (which I would expect to take a lot of memory), I just want students to be able to explore the output, and I need the package so they can access the custom
DESeqDataSet object. And I'm running into this problem before including the pre-computed results in my tutorial, so I'm pretty sure this is just from attaching the
DESeq2 package itself.
Reprex (I think, it's kind of hard to test this out and be sure):
DESeq2(a BioConductor package, install using
rsconnect, and a shinyapps.io account
- RStudio > File > New File > R Markdown... > From Template > Interactive Tutorial
library(DESeq2)to the tutorial setup block, and save.
- (In console), make sure shinyapps.io can install BioConductor packages:
options( repos=BiocManager::repositories() )
- Deploy App:
If I open the app, it looks okay, but the exercises don't work (nothing happens if I click "Run code"), and if I look at the logs for the app it says "Out of memory!"
Any idea why attaching a package in my tutorial would cause problems? If I run
library(DESeq2) locally in an R session, it only adds ~1MB according to
pryr::mem_used(). And I've been able to attach other packages in
learnr tutorials on shinyapps.io without a problem.